Package: bamsignals 1.39.0

Johannes Helmuth

bamsignals: Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Authors:Alessandro Mammana [aut, cre], Johannes Helmuth [aut]

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bamsignals.pdf |bamsignals.html✨
bamsignals/json (API)
NEWS

# Install 'bamsignals' in R:
install.packages('bamsignals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lamortenera/bamsignals/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:bamsignals-1.39.0(bioc 3.21)bamsignals-1.38.0(bioc 3.20)

dataimportsequencingcoveragealignmentcurlbzip2xz-utilszlibcpp

8.95 score 13 stars 12 packages 31 scripts 1.5k downloads 5 mentions 6 exports 20 dependencies

Last updated 2 months agofrom:df2b237eef. Checks:OK: 3 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 07 2024
R-4.5-win-x86_64OKDec 07 2024
R-4.5-linux-x86_64OKDec 07 2024
R-4.4-win-x86_64NOTEDec 07 2024
R-4.4-mac-x86_64NOTEDec 07 2024
R-4.4-mac-aarch64NOTEDec 07 2024
R-4.3-win-x86_64NOTEDec 07 2024
R-4.3-mac-x86_64NOTEDec 07 2024
R-4.3-mac-aarch64NOTEDec 07 2024

Exports:alignSignalsas.listbamCountbamCoveragebamProfilewidth

Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6RcppRhtslibS4VectorssysUCSC.utilsXVectorzlibbioc

Introduction to the bamsignals package

Alessandro Mammana and Johannes Helmuth

Rendered frombamsignals.Rmdusingknitr::rmarkdownon Dec 07 2024.

Last update: 2016-04-11
Started: 2015-02-13

Readme and manuals

Help Manual

Help pageTopics
Converts the container to a list 'l' such that 'l[[i]]' is the i-th signal.as.list.CountSignals
Efficient counting of reads in a bam filebamsignals-package bamsignals
Functions for extracting count signals from a bam file.bamCount bamCount,character,GenomicRanges-method bamCoverage bamCoverage,character,GenomicRanges-method bamProfile bamProfile,character,GenomicRanges-method bamsignals-methods
Container for count signalsalignSignals alignSignals,CountSignals-method as.list as.list,CountSignals-method CountSignals CountSignals-class length length,CountSignals-method width width,CountSignals-method [,CountSignals,ANY-method